Never used any tool for that. I crafted some initramfs and did it 
"manually" by building a static Busybox and recompiling the kernel with 
the proper options and the initramfs.conf file method. It is 
time-consuming if you're not skilled in scripting, which is my case, but 
you can insert the possibility of an interactive session in the 
initramfs, which eases debugging. Done like this, initramfs isn't a 
black box anymore. I wouldn't try to hack the initramfs of the distro; 
either use it as it is or craft my own.

     We are really talking of a corner case: one side of the corner is 
that you don't want initramfs; the other side is that you want to mount 
/usr separately. What's the reason for the last?

     As soon as you have /bin, /sbin and /lib, mounting /usr on a 
different partition for the purpose of sharing or snapshotting the OS 
doesn' work, because it would be only a part of the OS, which doesn't 
seem wise. What other reason? Size and access time of the filesystem 
seem both historical. Any other?

     Anyway I think there's a simple method to live without the 
initramfs. Everything which is done from initramfs could be done the 
same way from a disk partition, which might make it easier to debug: 
have a /os directory containing all the necessary subdirs, /os/proc, 
/os/sys, /os/dev, /os/run /os/usr, /os/lib, /os/var, /os/home... , mount 
the first five, create the few necessary files and symlinks and 
switch_root() to /os. This is exactly what your initramfs does.

     Didier